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Series GSE116202 Query DataSets for GSE116202
Status Public on Apr 29, 2019
Title TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [BS-seq]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, encoding the cytidine deaminase AID essential for CSR. TET enzymes deposit 5hmC, demethylate and maintain chromatin accessibility at two TET-responsive elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Transcriptional profiling identified BATF as the bZIP transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF recruits TET proteins to the Aicda enhancer. Our data emphasize the importance of TET enzymes for bolstering AID expression, and highlight 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.
Overall design 5hmC mapping by CMS-IP, ATAC-seq, RNA-seq, ChIP-seqs using B cells unstimulated or activated as a function time. Cells were either from WT or with Tet2/3 acutely deleted.
Contributor(s) Lio CJ, Shukla V, Gonzalez-Avalos E, Samaniego-Castruita D, Chakraborty A, Yue X, Schatz DG, Ay F, Rao A
Citation(s) 31028100
Submission date Jun 25, 2018
Last update date May 29, 2019
Contact name Anjana Rao
Organization name La Jolla Institute for Allergy and Immunology
Department Signaling and Gene Expression
Lab Anjana Rao
Street address 9420 Athena Cir
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (8)
GSM3213913 BS_WT_00h
GSM3213914 BS_WT_72h
GSM3213915 BS_DKO_00h
This SubSeries is part of SuperSeries:
GSE116208 TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer
BioProject PRJNA477775
SRA SRP151240

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Supplementary file Size Download File type/resource
GSE116202_OxBS_PostProbs_Formatted.txt.gz 1.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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